Clean Up function behaves like Layout when applied to reactions

**Description:**
The issue was discussed with Alexander Savelyev.
When Clean up function is applied to a reaction, the reaction changes its position as if Layout function is applied.

**Steps to reproduce:**
1. Create a reaction.
2. Distort the reaction.
3. Click "Clean Up" button.

**Actual result:**
Clean Up function behaves like Layout when applied to the reaction: the reaction changes its position on the canvas.

**Expected result:**
The reaction is cleaned up and undistorted. The reaction position is not changed.

Reproduce the issue by creating and distorting a reaction, then clicking the Clean Up button and comparing its behavior with Layout. Trace the Clean Up operation for reactions and verify that the reaction is undistorted without changing its canvas position.

Written by the indexing model from the issue text.